A briefing paper by the rights group on Tuesday described emaciated corpses delivered by the dozen to morgues, prison cells so crowded that detainees suffocated, inmates beaten so severely that they died or being taken out of the cells and shot.
The dead were suspected of being members of Boko Haram, a rebel group believed to be linked to Al Qaeda that is seeking to implement sharia, or Islamic law, across Nigeria. The group has been implicated in bombings and attacks on villages, schools and churches that have killed thousands of people in recent years.
Last month gunmen suspected of being from Boko Haram shot more than 50 sleeping students in a dormitory in Yobe state. The group opposes secular education and its name means “education is a sin” in the local Hausa language.
In July, Human Rights Watch said 3,600 people had died in conflict related to the Boko Haram uprising since 2009, including killings by the security forces.
Nigerian security forces have been criticized by rights groups in the past for its approach to the war on the Boko Haram, often firing randomly in civilian areas or arbitrarily rounding up young men as suspects.
Despite a heavy military presence in northern towns such as Maiduguri, Nigerian authorities have been struggling to contain the rebellion.
One reason why the militants have gained ground, critics argue, is that the heavy-handed tactics of the security forces create community resentment against authorities and engender support for the rebels. Amnesty International has previously reported on the arrests of hundreds of people in northern Nigeria who were held incommunicado for months without charge, trial or access to lawyers.
Amnesty International cited an unnamed senior military official as the source for the estimated 950 plus deaths in custody.
Many of the deaths happened in the military barracks in Maiduguri and other military facilities used by security forces as prisons for Boko Haram suspects. One of the facilities was nicknamed Guantanamo. Another was called the Guardroom.
Amnesty International interviewed 18 former detainees who said people died almost daily in detention “from suffocation or other injuries due to overcrowding and starvation. Some suffered serious injuries due to severe beating and eventually died in detention due to lack of medical attention and treatment.”
Others were shot during interrogations and left to bleed to death, according to the report. Some detainees were taken from their cells, when threats to shoot them were heard, and later did not return, according to the former detainees.
Amnesty International cited another unnamed senior military official confirming the high number of deaths.
“Hundreds have been killed in detention either by shooting them or by suffocation. … There are times when people are brought out on a daily basis and killed. About five people, on average, are killed nearly on a daily basis,” the officer told Amnesty International.
Amnesty International spokeswoman Lucy Freeman called on the Nigerian government to investigate the reported death toll.
“This is a staggeringly high figure that requires urgent action by the Nigerian government. The details of what happens behind locked doors in these shadowy detention facilities must be exposed, and those responsible for any human rights violations brought to book,” she said.
In April, Amnesty International workers counted 20 emaciated corpses with no gunshot wounds at the Maiduguri hospital morgue. Witnesses said security forces brought in the bodies and delivered corpses daily.
In another April incident, 60 corpses were delivered to a hospital morgue in Damaturu.
The briefing paper said human rights groups and activists were denied access to the detention facilities to reports on conditions.
“International standards, as well as Nigerian laws, require that deaths in custody must be investigated thoroughly and impartially," Freeman said. "Detainees have human rights and these must be respected in all instances.”